Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
☆251May 18, 2026Updated last week
Alternatives and similar repositories for treetime
Users that are interested in treetime are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Ultrafast Sample Placement on Existing Trees☆140May 10, 2026Updated 2 weeks ago
- Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins☆219Aug 27, 2025Updated 8 months ago
- Estimating time trees from very large phylogenies☆28Jul 21, 2024Updated last year
- An updated pipeline for pangenome investigation☆360May 13, 2026Updated last week
- IQ-TREE software version 2: phylogenetics by maximum likelihood☆330Mar 12, 2026Updated 2 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A collection of documented examples using TreeTime☆22Jul 30, 2019Updated 6 years ago
- snipit: summarise snps relative to your reference sequence☆173Jan 13, 2026Updated 4 months ago
- Finds SNP sites from a multi-FASTA alignment file☆279Dec 16, 2020Updated 5 years ago
- Reconstruction of transmission trees using genomic data☆72Sep 27, 2023Updated 2 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆65Jun 16, 2025Updated 11 months ago
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes☆121May 14, 2026Updated last week
- RAxML Next Generation: faster, easier-to-use and more flexible☆464Updated this week
- A bioinformatic toolkit to align genome assemblies into pangenome graphs☆125May 5, 2026Updated 3 weeks ago
- Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)☆30Jul 18, 2025Updated 10 months ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Create a tree using Mash distances☆188Oct 24, 2023Updated 2 years ago
- Parallel/Homoplasic SNP Finder☆20May 3, 2023Updated 3 years ago
- A tool for exploring large trees in the browser☆132May 7, 2026Updated 2 weeks ago
- Pipeline components for real-time phylodynamic analysis☆276May 19, 2026Updated last week
- A Nextflow pipeline for viral genomics (Influenza/RSV) supporting Illumina and Nanopore sequencing of clinical and wastewater samples.☆10May 15, 2026Updated last week
- The ARTIC fieldbioinformatics pipeline☆133Apr 28, 2026Updated 3 weeks ago
- Rapid determination of appropriate reference genomes.☆101Jan 22, 2025Updated last year
- Scalable relaxed clock phylogenetic dating☆27Sep 3, 2025Updated 8 months ago
- Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG☆21Feb 15, 2019Updated 7 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Finding regions of similarity between plasmids☆17Nov 2, 2022Updated 3 years ago
- Processing pipeline for pan-genome visulization and exploration☆145Oct 9, 2023Updated 2 years ago
- CFSAN Shigella Typing Pipeline☆15Jul 6, 2023Updated 2 years ago
- Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.☆146Apr 2, 2026Updated last month
- A toolbox for pangenome analysis and threshold evaluation.☆102Jul 8, 2022Updated 3 years ago
- ☆18Jun 11, 2024Updated last year
- Rapid & standardized annotation of bacterial genomes, MAGs & plasmids☆643May 15, 2026Updated last week
- Software package for assigning SARS-CoV-2 genome sequences to global lineages.☆454Apr 7, 2026Updated last month
- Split k-mer analysis – version 2☆104Apr 9, 2026Updated last month
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Reorients assembled microbial sequences☆137Aug 21, 2025Updated 9 months ago
- SARs-CoV-2 Primer schemes☆16May 14, 2025Updated last year
- baltic - adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. This fork will no longe…☆12Dec 18, 2019Updated 6 years ago
- ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads☆261Dec 13, 2025Updated 5 months ago
- an interactive viewer for populations of bacterial genomes linked by a phylogeny☆133Feb 26, 2024Updated 2 years ago
- Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement☆255May 5, 2026Updated 3 weeks ago
- Rapid haploid variant calling and core genome alignment☆585Dec 12, 2025Updated 5 months ago